Posts by Jeroen Van Goey

... I have the following FASTA file, `original.fasta`:
>foo
GCTCACACATAGTTGATGCAGATGTTGAATTCACTATGAGGTGGGAGGATGTAGGGCCA
I need to change the record id from `foo` to `bar`, so I wrote the following code:
from Bio import SeqIO
original_file = r"path\to\original.fasta"
corr ...

... I'm using dbFetch from EBI in a project. I construct URLs from the format
https://www.ebi.ac.uk/Tools/dbfetch/emblfetch?id=[ACCESSION_NUMBER]
to retrieve sequences, e.g.:
https://www.ebi.ac.uk/Tools/dbfetch/emblfetch?id=CO069431
Accession numbers need to be of the format 1 letter + 5 numerals O ...

... When using the SPAdes Genome Assembler, you can use either the BayesHammer read error correction tool for Illumina reads or the IonHammer read error correction tool for IonTorrent data.
I want to use SPAdes in a general workflow and I want to know if there is an automatic way to determine if reads ...

... http://anthonyneedsajob.com/
What happened?
Anthony (Biostar user page) will soon start on an adventure in an exciting startup, but starting 1st of October 2013, he has no real source of income.
Since Anthony can not sit on his hands, he is now looking for partners to tackle exciting technical pr ...

... r.id in the line `
records = (r for r in SeqIO.parse(input_file, "fasta") if r.id in wanted)
gives back something from the form 'gnl|TC-DB|P0A334'. So, just changing that line to
records = (r for r in SeqIO.parse(input_file, "fasta") if r.id.split('|')[2] in wanted)
will work. I will assume th ...

... Are you following the Entrez Usage Guidlines? Specifically:
For any series of more than 100 requests, do this at weekends or
outside USA peak times. This is up to you to obey.
Make no more than three requests every seconds (relaxed from at most one request every three seconds in early 2009). Thi ...

... The project that Nikolay Vyahhi metioned that he was working on has gone live in the meantime: rosalind.info is a Project Euler like website with lots of small bioinformatics programming problems. It doesn't have the student/expert matching component though.
...